The diversity of the genus Trichomycterus Valenciennes 1832 in the Rio Doce basin is investigated using conventional and modern morphology and DNA analyses. The work is presented in two Chapters. Chapter One, entitled Diversity of the genus Trichomycterus Valenciennes, 1832 (Siluriforms, Trichomycteridae) in the Rio Doce basin: a systematic study integrating phenotypes, DNA and classical taxonomy integratively analyzes specimens of the genus from the entire Rio Doce drainage and adjacent basins, both from available world-wide collections and from active sampling efforts. A combination of phenotypic and DNA (COI barcoding analysis) provides evidence for the existence of 14 species in the basin, 10 of which are new: T. alternatus Eigenmann, 1917; T. argos Lezama et al., 2012; T. astromycterus sp. nov.; T. barrocus sp. nov.; T. brucutu sp. nov.; T. brunoi Barbosa & Costa, 2010; T. immaculatus (Eigenmann & Eigenmann, 1889)] T. illuvies sp. nov.; T. melanopygius sp. nov.; T. ipatinguensis sp. nov.; T. pussilipygius sp. nov.; T. sordislutum sp. nov.; T. vinnulus sp. nov; and T. tantalus sp. nov. . In addition, a lectotype is designated for T. immaculatus and the species is considered as a senior synonym of Trichomycterus pradensis Sarmento-Soares et al., 2005. Although remarkable, such increase in species number of Trichomycterus in a single drainage matches similar recent increments in some other Southeastern Brazilian basins, such as the Paraíba do Sul and Iguaçu. The kind of differentiation among species herein recognized varies, with some of them being well-differentiated in morphology but not in barcoding data, and others showing the opposite phenomenon. The geographical distribution of each of the 14 species is plotted in the Rio Doce basin. The wide geographical distribution of some species (T. alternatus and T. immaculatus) is explained against data from geomorphological processes and comparative information on their biology. Chapter two, The type specimens of Trichomycterus alternatus (Eigenmann, 1917) and T. zonatus (Eigenmann, 1918), with elements for future revisionary work (Teleostei, Siluriformes, Trichomycteridae) focuses on the complex taxonomy, nomenclature and type material status of T. alternatus and T. zonatus. The type series of the two species are analyzed in detail, both in morphology and locality data. Osteological information was obtained with conventional and a new technique of radiographic stereo-triplets. Our new data elucidates their species distinctiveness, diagnostic characteristics, type localities and show that T. zonatus does not occur in the Rio Doce basin. / A diversidade do gênero Trichomycterus Valenciennes 1832 na bacia do Rio Doce é investigada utilizando métodos convencionais e modernos em análises morfológicas e moleculares. Os resultados desta dissertação são apresentados em dois capítulos. Capítulo um, intitulado Diversity of the genus Trichomycterus Valenciennes, 1832 (Siluriforms, Trichomycteridae) in the Rio Doce basin: a systematic study integrating phenotypes, DNA and classical taxonomy examinou espécimes pertencentes a este gênero encontrados no Rio Doce e em bacias adjacentes disponíveis em coleções nacionais e internacionais e coletados durante esta dissertação. O conjunto de dados obtidos através de análises morfológicas e moleculares (COI, DNA barcoding) revelou a existência de 14 espécies na bacia do Rio Doce, das quais 10 novas: T. alternatus Eigenmann, 1917; T. argos Lezama et al., 2012; T. astromycterus sp. nov.; T. barrocus sp. nov.; T. brucutu sp. nov.; T. brunoi Barbosa & Costa, 2010; T. immaculatus (Eigenmann & Eigenmann, 1889)] T. illuvies sp. nov.; T. melanopygius sp. nov.; T. ipatinguensis sp. nov.; T. pussilipygius sp. nov.; T. sordislutum sp. nov.; T. vinnulus sp. nov; and T. tantalus sp. nov. Além disso, é designado um lectótipo para T. immaculatus, espécie aqui proposta como sinônimo sênior de Trichomycterus pradensis Sarmento-Soares et al., 2005. O acentuado incremento em número de espécies de Trichomycterus para uma única bacia segue um padrão de crescimento em biodiversidade conhecida do gênero para outras drenagens do sudeste brasileiro a exemplo do rio Paraíba do Sul e Iguaçu. Os tipos de diferenciação detectada entre as espécies aqui tratadas variam, com algumas bem corroboradas morfologicamente, porém muito similares ou indiferenciáveis em análise de DNA barcoding, e outras apresentando o fenômeno oposto. As distribuições geográficas de cada uma das 14 espécies são mapeadas com base em todo o material examinado. A ampla distribuição geográfica de algumas espécies (T. alternatus and T. immaculatus) é explicada através de processos geomorfológicos e informações comparativas sobre suas biologias. O capítulo dois, The type specimens of Trichomycterus alternatus (Eigenmann, 1917) and T. zonatus (Eigenmann, 1918), with elements for future revisionary work (Teleostei, Siluriformes, Trichomycteridae) se concentra em esclarecer a complexa taxonomia, nomenclatura e o status do material tipo de T. alternatus e T. zonatus. As séries tipos das duas espécies foram minuciosamente analisadas tanto para morfologia como para suas respectivas localidades de proveniência. Informações osteológicas foram obtidas através de técnicas de radiografia convencionais e uma nova metodologia chamada stereo triplets. Os dados obtidos corroboram as respectivas espécies como distintas, e permitem uma avaliação precisa de seus respectivos caracteres diagnósticos e localidades tipo. Também se chegou à conclusão que T. zonatus não ocorre na bacia do Rio Doce.

Les pycnogonides sont une classe d’arthropodes marins comptant plus de 1 400 espèces, et dont nous connaissons mal la diversité et l’histoire évolutive. Cette thèse pluridisciplinaire sur les pycnogonides tropicaux s’articule autour de quatre axes de recherche : (i) description de neuf fossiles de Solnhofen (Jurassique supérieur), grâce à une nouvelle technique de visualisation des volumes ; (ii) analyses phylogénétiques des gènes CO1 et 18S à partir de 107 taxons ; (iii) séquençage Illumina par shotgun et assemblage de 103 nouveaux génomes mitochondriaux ; et (iv) taxonomie intégrative des pycnogonides de Martinique reposant sur 803 spécimens collectés lors de l’expédition Madibenthos (2016) et 172 séquences CO1. Tous les fossiles de Solnhofen étudiés sont rattachés aux pantopodes, marquant leur affinité avec la faune moderne. Deux espèces nouvelles sont décrites. Avec les fossiles de La Voulte-sur-Rhône, ils montrent que les pantopodes étaient déjà diversifiés dans des eaux profondes et lagunaires du Jurassique, suggérant une importante transition de faune entre Paléozoïque et Mésozoïque. De nombreux réarrangements du génome mitochondrial, impliquant principalement les gènes des ARNt, sont mis en évidence. Certains sont corrélés à des changements dans le biais de composition en bases qui peuvent impacter la reconstruction phylogénétique. Malgré ces problèmes, nous retrouvons la monophylie de toutes les familles excepté les Ascorhynchidae, Callipallenidae et Nymphonidae, et identifions des regroupements interfamiliaux, d’un côté entre Ammotheidae, Pallenopsidae, Endeidae et Phoxichilidiidae, et de l’autre, entre Callipallenidae et Nymphonidae. Un très grand nombre de relations intergénériques et interspécifiques est également révélé. Alors que 20 espèces étaient auparavant connues sur les côtes de Martinique, cette étude a permis de multiplier par quatre la diversité connue de l’île, soit un total de 73 espèces. Ces résultats suggèrent une diversité encore plus importante à l’échelle des Caraïbes, que l’on pensait pourtant bien explorées. / Sea spiders are a class of marine arthropods including more than 1,400 species. Their diversity and evolutionary history are still poorly known. In this thesis, tropical pycnogonids were studied using four approaches: (i) nine fossils from Solnhofen (Upper Jurassic) were examined using a new photographic technic improving visualization of body parts; (ii) for phylogeny, CO1 and 18S genes were analyzed for 107 taxa; (iii) 103 new mitochondrial genomes were assembled after Illumina shotgun sequencing; and (iv) 803 sea spiders collected during the Madibenthos expedition (2016) in Martinique were examined for integrative taxonomy using 172 CO1 sequences.All fossils from Sonhofen are shown to share strong affinities with the modern fauna, as they were identified as belonging to Pantopoda. Two new species are described. Together with fossils from La Voulte-sur-Rhône, these results suggest that Pantopoda were already diversified in shallow and deep Jurassic waters, indicating that an important faunal transition occurred between Palaeozoic and Mesozoic. The mitochondrial genome of sea spiders shows many different gene orders and most of the gene rearrangements involve tRNA genes. Some are correlated with changes in base composition bias, which can be misleading for phylogenetic reconstruction. Despite these problems, all families but Ascorhynchidae, Callipallenidae and Nymphonidae were found to be monophyletic. Furthermore, our analyses provide evidence for several interfamilial relationships (between Ammotheidae, Pallenopsidae, Endeidae and Phoxichilidiidae; and between Callipallenidae and Nymphonidae), and for many intergeneric and interspecific relationships. While only 20 pycnogonid species were previously known from Martinique, the number of species was multiplied by four after our study, i.e. 73. These results suggest that many species still remain to be discovered in the Caribbean Sea, whereas this region was thought to be well-explored regarding sea spiders.

Le Plateau des Guyanes a été géologiquement stable au cours de l'ère Cénozoïque, exempt de l'influence de l'orogénèse des Andes et de la mise en place du bassin de l'Amazone. Cette région est-elle biogéographiquement homogène au sein de l'Amazonie ? Quelles sont les modalités spatio-temporelles de diversification au sein de cette région ? Afin de répondre à ces questions, j'ai exploré sa biorégionalisation sur la base de la distribution des amphibiens anoures. Cette approche a permis de définir trois biorégions dans l'est du Plateau des Guyanes, et de révéler une forte sous-estimation de l'endémisme. Ensuite, j'ai étudié les patrons de diversification au sein du genre endémique Anomaloglossus. Ce volet a permis de dévoiler l'existence de spéciation cryptique au sein du genre, avec un patron biogéographique composé de quatre zones de diversification au sein du Plateau des Guyanes et une origine du genre dans les tepuis. / The Guiana Shield has been geologically stable during the Cenozoic era, exempt of the influence of the uplift of the Andes and the setting up of the Amazon basin. Is this region biogeographically homogeneous within Amazonia? What are the spatio-temporal diversification modalities within this region? To answer these questions, I explored bioregionalisation within Amazonia and the Guiana Shield based on the dis- tribution of anuran amphibians. This approach enabled to define three bioregions in the eastern Guiana Shield and to reveal a high underestimation of endemism. Then, I studied the diversification patterns within the endemic frog genus Anomaloglossus. This part en- abled to reveal cryptic speciation within the genus, and a biogeographic pattern composed of four areas of diversification in the Guiana Shield, with an origin of the genus in the western highlands (tepuis).

Free-living marine nematodes are the most ubiquitous, abundant and diverse meiofaunal component of benthic communities. These are excellent model organisms, due to its short life span, wide availability and feasibility to cultivate with minimum laboratory facilities. In this study, a population of Diplolaimella dievengatensis Jacobs 1991 (Nematoda, Monhysteridae) from the relatively Pristine estuary of the Guaratuba River in São Paulo, Brazil was isolated and cultivated. The goals were; i- to apply an integrative taxonomic approach in order to compare this population from Brazil with another from the species type-locality in the Belgian Coast, with regard to morphological, life-cycle and the 18S gene of the rDNA molecular data; and ii- to compare, at the light of life history theory, the responses of life history parameters such as; fecundity, growth and survivorship of D. dievengatensis (here as a slower species) and Litoditis marina (Bastian, 1865) (Nematoda, Rhabditidae) (as a faster species) under sublethal exposition to the sodium dodecyl sulfate (SDS) surfactant. The population from Brazil was similar to that from Belgium coast in all parameters. Although morphometric analyses considered the Brazilian D. dievengatensis isometrically larger than the Belgian population regarding some characters, the presence of all diagnostic characters confirmed the similarity of both species. The life-cycle, hatching time, final body length, and biomass parameters were similar in both populations, in which females were larger than males. The population growth, measured as intrinsic rate of natural increase was slightly higher for the D. dievengatensis from Brazil (rm=0.41), than the European population (rm =0.348). Molecular comparison on Genbank showed 99.4% of similarity between both populations, indicating therefore, that D. dievengatensis from Brazil is similar to those from Belgium. In the chapter ii, both species responded differently to SDS exposition. Growth and reproduction rate of D. dievengatensis surprisingly were enhanced at low and intermediate concentrations of SDS (0.001 and 0.003%), while for L. marina these parameters were reduced in all SDS concentrations tested (0.001, 0.003 and 0.006%). The SDS did not affect the survivorship of adults of the slower specie. On the other hand, survivorship of adults of the fast species was significantly affected by SDS and this effect was dependent on adult gender, with reduced rates of males exposed to 0.006% SDS. Although both species are located nearby along the fast-slow continuum, they responded distinctly to of the toxic SDS effect. Effects over L. marina met the trend of faster species in allocating fewer investments in defenses against physiological injuries and on their own somatic maintenance. We propose that the apparent lower resistance of this faster species under stress at the individual level is balanced by their higher reproductive rates, conferring higher resilience to this species at the population level. Finally, it was demonstrated that the marine nematode D. dievengatensis is an important native model organism which can be used in a wide range of studies and experimental tests. Identifying and understanding differential effects of stress in the context of life-history theory is an important aspect which enhanced our understanding about the threats posed by anthropogenic activities on natural communities / Nematodas marinhos de vida livre são o mais onipresentes, abundantes e diversos componentes da meiofauna em comunidades bênticas. São excelentes organismos modelo devido a seu curto ciclo de vida, ampla disponibilidade e viabilidade de cultivo com mínima estrutura laboratorial. Neste estudo, uma população de Diplolaimella dievengatensis Jacobs 1991 (Nematoda, Monhysteridae) do estuário relativamente prístino do rio Guaratuba, São Paulo, Brasil foi isolada e cultivada. Os objetivos foram: ii- aplicar uma abordagem taxonômica integrativa a fim de comparar esta população do Brasil com outra da localidade tipo dessa espécie, da costa da Bélgica, com relação à dados morfológicos, do ciclo de vida e molecular do gene 18S do rDNA; e ii-comparar, à luz da teoria da historia de vida, repostas de parâmetros do ciclo de vida tais como: fecundidade, crescimento e sobrevivência de D. dievengatensis (aqui como espécies mais lenta) e Litoditis marina (Bastian, 1865) (Nematoda, Rhabditidae) (como espécie rápida) sob exposição subletal ao surfactante dodecil sulfato de sódio (DSS) . A população do Brasil foi similar a da costa da Bélgica em todos os parâmetros. Embora analises morfométricas consideraram D. dievengatensis do Brasil isometricamente maior que a população belga em relação em algumas características, a presença de todos os caracteres diagnósticos confirmaram a similaridade de ambas as espécies. Os parâmetros de ciclo de vida, tempo de eclosão, comprimento corporal final e biomassa foram similares em ambas as populações, nas quais fêmeas foram maiores que machos. Crescimento populacional, mensurado como taxa intrínseca de crescimento natural foi ligeiramente mais alta para D. dievengatensisdo Brasil (rm=0.41), que para a população europeia (rm=0.348). Comparações moleculares no Genbank mostraram 99.4% de similaridade entre ambas populações, indicando portanto que a população do Brasil é similar a D. dievengatensis belga. No capítulo ii, ambas as espécies responderam distintamente a exposição ao SDS. Supreendentemente as taxas de crescimento e de reprodução de D. dievengatensis foram incrementadas sob concentrações mais baixas e intermediárias (0.001 e 0.003%), enquanto para L. marina esses parâmetros foram reduzidos em todas as concentrações de DSS testadas (0.001, 0.003 e 0.006%). O DSS não afetou a sobrevivência de adultos da espécie mais lenta. Por outro lado, a sobrevivência de adultos da espécie mais rápida foi significativamente afetada pelo SDS e esse efeito foi dependente do sexo, com taxas reduzidas em machos expostos a 0.006 % de DSS. Embora ambas as espécies estejam proximamente dispostas ao longo do gradiente \"rápido-lento\", elas responderam diferentemente ao efeito tóxico do DSS. Efeitos sobre L marina se enquadram no padrão de espécies mais rápidas ao alocar menores investimentos para as defesas contra danos fisiológicos e para sua própria manutenção somática. Nós propomos que a aparente menor resistência desta espécie rápida sob estresse ao nível individual é balanceada por suas altas taxas reprodutivas, conferindo mais alta resiliência a essa espécie ao nível populacional. Por fim, foi demonstrado que D. dievengatensis é um importante organismo modelo nativo que pode ser usado em uma ampla diversidade estudos e testes experimentais. Identificar e compreender diferentes efeitos do estresse dentro do contexto da teoria da história de vida é um aspecto importante, o qual tem aumentado nosso conhecimento sobre as ameaças de atividades antropogênicas sobre comunidades naturais

Ammomanes cinctura (Bar-tailed Lark) is a lark species with a wide distribution in the Palearctic. One of its subspecies, A. c. arenicolor, has a wide range across northern Africa, within which it shows very minor morphological variation but deep divergence in the mitochondrial cytochrome b locus between two geographically widely separated populations. There are two additional allopatric subspecies, A. c. cinctura (Cape Verde Islands) and A. c. zarudnyi (Iran to Pakistan), which differ slightly more in morphology. The genomic population structure, evolutionary history, and taxonomic status of the different populations within this species remain unclear. I applied an integrative approach, using genomic single nucleotide polymorphisms (SNPs), mtDNA and morphological data, to investigate the evolutionary divergence within Ammomanes cinctura. I acquired whole-genome sequence data from twelve individuals from Morocco (n=2), Saudi Arabia (n=7), and Iran (n=3), and performed phylogenetic and population structure analyses. Mitochondrial genomes were assembled and cytochrome b was extracted for phylogeny. Biometric measurements and quantified plumage analysis were conducted on museum specimens of all three subspecies. According to the mitochondrial data, the samples from Saudi Arabia and Iran form a clade that is deeply diverged (5.94 Mya, 95%HPD 3.15–8.95 Mya) from a clade comprising the samples from Morocco and Cape Verde Islands. In contrast, the nuclear SNPs recovered a very shallow divergence (0.095 Mya, 95%HPD 0.04-0.16 Mya) and weak population structure between the samples from Morocco vs. Saudi Arabia–Iran. Morphological results indicated that zarudnyi is slightly differentiated from the other two subspecies, with a larger body size, and the three subspecies are slightly divergent in plumage. The close similarity between Moroccan and Saudi Arabian birds in morphology was also confirmed, in conflict with the molecular data – highlighting the problem with trinomials in this case. The results suggest that the deep divergence in mitochondrial DNA is due to a complex evolutionary history.

As vocalizações em anuros são comumente conspícuas e, até certo ponto, estereotipadas. Nesse grupo, o principal sinal acústico emitido por machos (canto de anúncio) basicamente codifica dois tipos de informação: a atração de fêmeas coespecíficas e o anúncio da posição do macho em atividade de vocalização, especialmente relevante na orientação espacial e delimitação de sítios de vocalização em espécies territoriais. Mais modernamente, com o devenvolvimento de métodos computacionais para incorporar a informação filogenética disponível para um dado grupo de organismos, tornou-se factível explorar tendências evolutivas e testar hipóteses adaptivas para de maneira mais apropriada, levando em conta a dependência filogenética dos táxons. Leptodactylinae é um grupo de anuros Neotropicais rico em espécies (ca. 95 spp.), cuja distribuição está essencialmente compreendida na região Neotropical. Esse táxon apresenta uma diversidade notável de vocalizações. A diversidade de padrões acústicos em Leptodactylidae por si só ressalta o potencial desse táxon representar um bom modelo para estudos focados no entendimento dos padrões e processos macroevolutivos envolvidos na evolução acústica nesse grupo de vertebrados. Nesse estudo, foi realizada uma revisão detalhada dos sinais acústicos reprodutivos, i.e. canto de anúncio, pela primeira vez analisados para esse táxon através de procedimentos e configurações padronizadas e com quantificações automatizadas. Os resultados das análises acústicas foram então associados aos padrões morfológicos na investigação dos padrões de diversidade críptica e reavaliação taxonômica de algumas populações e espécies em Leptodactylinae, além da abordagem comparativa a partir dos resultados obtidos das análises acústicas a fim de explorar as principais tendências e processos evolutivos dos sinais acústicos nesse grupo de anuros. Os resultados revelaram que existem diferentes padrões de diferenciação fenotípica nesse táxon, apontando para a necessidade de revisões taxonômicas em diferentes clados de Leptodactylinae, com resultados contundentes para o clado L. melanonotus (a reavaliação de sinônimos juniores nesse clado indicaram que duas espécies devem ser revalidadas) e Adenomera (reconhecimento de diversidade críptica em A. hylaedactyla com base em evidência acústica). A exploração de métodos comparativos filogenéticos relevou tendências evolutivas interessantes, como, por exemplo, os surgimentos e desaparecimentos recorrentes de estruturas temporais (pulsos) e mudanças acentuadas na estrutura espectral dos sinais acústicos (deslocamento da frequência fundamental em algumas espécies de Adenomera), tais fenômenos sem relação aparente com tamanho corporal ou estrutura dos habitats ocupados por essas espécies. Os dados acústicos oriundos desse estudo se mostraram eficazes nas resoluções taxonômicas em várias espécies de Leptodactylinae. Estudos futuros focando em aspectos da morfologia do aparato vocal, e biomecânica de produção de som, podem informativos acerca do entendimento dos processos envolvidos em distintos padrões acústicos reconhecidos em Leptodactylinae / In anurans, vocalizations are usually conspicuous and stereotyped to some extent. In this group, the major acoustic signal broadcast by males (advertisement signal/call) basically encodes two kinds of information: the attraction of conspecific females and the advertisement of the position of a calling male, maintaining male spacing functioning as an auditory cue in the delimitation of calling sites in territorial species. More recently, the development of computational methods as a means of incorporation of phylogenetic information available for a given group of organisms allowed scientists to explore evolutionary trends and to test for adaptative hypotheses more properly, taking into consideration phylogenetic dependence among taxa. Leptodactylinae is a species-rich taxon (ca. 95 spp.), whose distribution encompasses the Neotropical region. This frog group exhibits a remarkable diversity of vocalizations. This pattern in Leptodactylinae draws attention to the fact that this group could be a promising model organism to studies focused on macroevolutionary patterns and processes involved in the acoustic evolution in this vertebrate group. In the present study, a comprehensive acoustic review was conducted, and it was the first time for this group that the analytical procedures and standardized settings were employed in an automated fashion for the quantification of acoustic traits. The results of the acoustic analysis was then associated with morphological patterns as a means to investigate the patterns of cryptic diversity and taxonomic reappraisals for some populations and species, as well as the application of comparative methods from the results obtained to explore the major evolutionary trends and processes of acoustic traits in this frog group. The results revealed that there are distinctive patterns of phenotypic differentiation present across Leptodactylinae clades, which indicate that taxonomic reassessments are required, particularly in the L. melanonotus clade (revaluation of the junior synonyms showed that two species should be relavalidated) and Adenomera (cryptic diversity was uncovered under the name A. hylaedactyla based on acoustic evidence). The phylogenetic comparative methods recovered interesting evolutionary trends as, for instance, the convergent appearances and losses of structures related to the time domain (pulses) and remarkable changes in the frequency domain (doubling of the fundamental frequency in some species of Adenomera), both phenomena being apparently unrelated to differences in body size or calling habitats. The acoustic data gathered here was efficient in species discrimination and should represent a good line of evidence to address species-level taxonomy in Leptodactylinae. Future research focused on aspects of the vocal apparatus and the mechanisms of sound production might tell us more about the evolutionary processes involved in the distinctive acoustic patterns that were recognized in Leptodactylinae

Pontoscolex corethrurus est le ver de terre le plus répandu dans les zones tropicales et sub-tropicales ; il est par conséquent très étudié en science du sol. Il est présent dans toutes sortes d’habitats, des sols pauvres de prairie aux sols riches de forêt primaire, et ses caractéristiques écologiques sont bien connues. Ses caractéristiques biologiques ont été moins étudiées. Peu de données sur la variation génétique au sein de cette morphoespèce sont disponibles à l’exception de la découverte en 2014 de deux lignées génétiquement différentes dans l’île São Miguel des Açores. De plus, son degré de ploïdie n’est pas connu et sa stratégie de reproduction n’est pas bien décrite. L’un des objectifs de cette thèse était de comprendre les mécanismes et les caractéristiques qui font de P. corethrurus un envahisseur efficace. Notre deuxième objectif était de rechercher des lignées cryptiques dans le monde entier et de décrire leurs relations phylogénétiques. Un troisième objectif était d’identifier quelle lignée était invasive et de caractériser la structure génétique de ses populations dans les aires native et d’introduction. Le dernier objectif était de tester si les différentes espèces du complexe avaient différents degrés de ploïdie, ce qui pourrait expliquer l’isolement reproducteur entre ces espèces. Une synthèse bibliographique de 265 études couvrant tous les aspects des connaissances sur P. corethrurus a montré que la stratégie – r et la plasticité de ce ver sont les caractéristiques clefs qui lui permettent d’envahir avec succès différents habitats. Afin d’étudier la diversité cryptique au sein de P. corethrurus à une échelle mondiale, j’ai examiné 792 spécimens collectés dans 25 pays et îles différents. Ces spécimens ont été analysés à l’aide de deux marqueurs mitochondriaux (COI et ADNr 16S), deux marqueurs nucléaires (internal transcribed spacers 2 et ADNr 28S) et une matrice de données de séquence multilocus obtenue à l’aide de la méthode AHE (Anchored Hybrid Enrichment). De plus, un total de 11 caractères morphologiques, internes comme externes, ont été étudiés dans toutes les lignées caractérisées génétiquement. Quatre espèces cryptiques (L1, L2, L3 et L4) ont été observées au sein du complexe d’espèces P. corethrurus. Elles ont été trouvées en sympatrie dans plusieurs localités et des analyses basées sur des marqueurs AFLP n’ont pas montré d’hybridation entre L1 et L3. La possibilité d’isolement reproducteur lié à des degrés de ploïdie différents a été évaluée à l’aide d’expérimentations de cytogénétique pour lesquelles plusieurs obstacles ont été rencontrés, à différentes étapes. Des résultats n’ont été obtenus que pour L4 (2n = 70). L’une des espèces du complexe, L1, était géographiquement répandue. Cette espèce correspondait aux spécimens topotypiques (échantillons provenant du jardin de Fritz Müller où P. corethrurus a été décrit en premier en 1856). Nous avons ciblé cette espèce invasive dans une étude de génétique des populations et de phylogéographie. En utilisant le gène COI et des marqueurs AFLP, nous avons révélé une faible diversité génétique dans la zone tropicale, probablement due à des évènements de colonisation récents et à une reproduction asexuelle. Cependant, la diversité génétique relativement élevée dans certaines populations, associée à un déséquilibre de liaison relativement faible, suggère aussi des évènements de reproduction sexuelle. A ce jour, c’est le premier travail réalisé à l’échelle mondiale sur la diversité génétique cryptique, la génétique des populations et la phylogéographie d’une espèce de vers de terre pérégrine dans la zone tropicale. J’ai produit la première revue complète des caractéristiques de P. corethrurus. De plus, son statut taxinomique a été clarifié ainsi que sa stratégie de reproduction qui est mixte (parthénogénèse et amphimixie). Ces informations seront utiles pour les expérimentations et les recherches futures sur les espèces du complexe P. corethrurus / Pontoscolex corethrurus is the most widespread earthworm species in the tropical and sub-tropical zones, it is hence one of the most studied earthworm in soil science. Ecological aspects of P. corethrurus, which is known to be present in a wide range of habitats from poor soils of pasture to rich soils of primary forest, were intensively investigated but biological aspects are less addressed. In particular, information on the genetic variation within the morphospecies is scarce except for the finding of two genetically differentiated lineages in São Miguel Island of Azores archipelago in 2014. Moreover, the ploidy degree of the morphospecies is not yet known and its reproduction strategy is not well understood. One of the objectives of this thesis was to understand the mechanisms and characteristics which make P. corethrurus a successful invader. Our second objective was to look for cryptic lineages in the whole world and to describe the phylogenetic relationships between them. A third objective was to identify which lineage was invasive and to characterize its population genetic structure in the native and the introduced ranges. The last objective was to test if the different species of the complex have different ploidy degrees (polyploid complex). This could eventually explain the reproductive isolation among these species. A bibliographic synthesis of 265 studies covering all subjects of knowledge on P. corethrurus showed that the r strategy and plasticity of this earthworm are the key characteristics which make it a successful invader in different habitats. In order to investigate the cryptic diversity within P. corethrurus in a world-wide scale, I examined 792 specimens collected from 25 different countries and islands. These specimens were analyzed using two mitochondrial (COI and 16S rDNA) and two nuclear (internal transcribed spacers 2 and 28S rDNA) markers and a large-scale multilocus sequence data matrix obtained using the Anchored Hybrid Enrichment (AHE) method. In addition, a total of 11 morphological characters, both internal and external, were investigated in all genetically characterized lineages. Four cryptic species (L1, L2, L3 and L4) were found within the P. corethrurus species complex, and four potentially new species within the genus Pontoscolex. The cryptic species were observed in sympatry at several localities, and analyses based on AFLP markers showed no hybridization among L1 and L3. The possibility of reproductive isolation among species of the complex because of different ploidy degrees was investigated by cytogenetic experimentations. Due to different obstacles encountered at different steps of the experimentations, results were just obtained for L4 (2n=70). One of the species belonging to the complex, L1, was particularly widespread per comparison with the others. This species corresponded to topotype specimens (samples from Fritz Müller’s garden where P. corethrurus was first described in 1856). Thus, we focused on this invasive species in a population genetics and phylogeography study. Using COI gene and AFLP markers, we revealed low genetic diversity through the tropical zone, probably due to recent colonization events and asexual reproduction type. Meanwhile, due to weak linkage disequilibrium and relatively high genetic diversity in some populations, sexual reproduction was suggested for L1.To date, this is the first study investigating at a world-wide scale, cryptic species diversity, population genetics and phylogeography of a peregrine earthworm species throughout tropical zone. I produced the first comprehensive review of all ecological and biological aspects of P. corethrurus. Moreover, the taxonomic status of P. corethrurus was clarified as well as its reproduction strategy which is mixed (parthenogenetic and sexual). All these findings represent potentially useful information for future experimentations and researches on species of P. corethrurus complex

No description available.

The Rufous-naped lark Mirafra africana complex consists of 22 subspecies spread across the African continent. Several of the subspecies have recently been suggested to potentially be treated as separate species. In this study a comparative analysis was done on the song from seven of the subspecies: M. a. africana, M. a. athi, M. a. grisescens, M. a. kabalii, M. a. nyikae, M. a. transvaalensis and M. a. tropicalis. The results showed that M. a. athi, M. a. kabalii and M. a. nyikae are all very divergent from each other as well as from the other four subspecies. In contrast, M. a. tropicalis, M. a. grisescens, M. a. africana and M. a. transvaalensis are not clearly separable from each other. Based on the results, I suggest that M. a. athi, M. a. kabalii and M. a. nyikae can be classified as separate species, with M. a. africana, M. a. tropicalis, M. a grisescens and M. a. transvaalensis forming a fourth species (M. africana sensu stricto). Finally, I conclude that this study shows that more studies need to be done on the subspecies of the Mirafra africana complex.

No description available.